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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4
author iuc
date Wed, 03 Dec 2025 15:44:18 +0000
parents 46bca620b895
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2:46bca620b895 3:1316b4fa3c4c
1 <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT"> 1 <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description>for automated alignment trimming</description> 2 <description>for automated alignment trimming</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.5.0</token> 4 <token name="@TOOL_VERSION@">1.5.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">23.0</token>
6 </macros> 7 </macros>
7 <edam_topics> 8 <edam_topics>
8 <edam_topic>topic_3293</edam_topic> <!-- phylogenetics --> 9 <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->
9 <edam_topic>topic_0080</edam_topic> <!-- sequence analysis --> 10 <edam_topic>topic_0080</edam_topic> <!-- sequence analysis -->
10 </edam_topics> 11 </edam_topics>
70 -sst 71 -sst
71 -sident 72 -sident
72 -soverlap 73 -soverlap
73 | tee '$statsout' 74 | tee '$statsout'
74 #end if 75 #end if
75
76
77 ]]></command> 76 ]]></command>
78 <inputs> 77 <inputs>
79 <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" /> 78 <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)"/>
80 <conditional name="trimming_mode"> 79 <conditional name="trimming_mode">
81 <param name="mode_selector" type="select" label="Select trimming mode from the list"> 80 <param name="mode_selector" type="select" label="Select trimming mode from the list">
82 <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option> 81 <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>
83 <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option> 82 <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option>
84 <option value="-gappyout">gappyout - only uses information based on gaps' distribution.</option> 83 <option value="-gappyout">gappyout - only uses information based on gaps' distribution.</option>
86 <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option> 85 <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option>
87 <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option> 86 <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option>
88 <option value="custom">custom mode - define trimming parameters yourself.</option> 87 <option value="custom">custom mode - define trimming parameters yourself.</option>
89 <option value="manual">manual mode - specify columns or sequences to remove</option> 88 <option value="manual">manual mode - specify columns or sequences to remove</option>
90 </param> 89 </param>
91 <when value="-nogaps" /> 90 <when value="-nogaps"/>
92 <when value="-noallgaps"/> 91 <when value="-noallgaps"/>
93 <when value="-gappyout"/> 92 <when value="-gappyout"/>
94 <when value="-strict"/> 93 <when value="-strict"/>
95 <when value="-strictplus"/> 94 <when value="-strictplus"/>
96 <when value="-automated1"/> 95 <when value="-automated1"/>
107 <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/> 106 <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/>
108 <param argument="-conthreshold" type="float" optional="true" min="0" max="100" label="Consistency Threshold. Minimum consistency value required" help="Range: [0 - 1]. Not allowed in combination with inputfile."/> 107 <param argument="-conthreshold" type="float" optional="true" min="0" max="100" label="Consistency Threshold. Minimum consistency value required" help="Range: [0 - 1]. Not allowed in combination with inputfile."/>
109 <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/> 108 <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/>
110 <param argument="-clusters" type="integer" optional="true" min="0" label="Clusters. Get the most Nth representatives sequences from a given alignment." help="Range: [1 - (Number of sequences)]"/> 109 <param argument="-clusters" type="integer" optional="true" min="0" label="Clusters. Get the most Nth representatives sequences from a given alignment." help="Range: [1 - (Number of sequences)]"/>
111 <param argument="-maxidentity" type="float" optional="true" min="0" max="1" label="Max Identity. Get the representatives sequences for a given identity threshold. " help="Range: [0 - 1]"/> 110 <param argument="-maxidentity" type="float" optional="true" min="0" max="1" label="Max Identity. Get the representatives sequences for a given identity threshold. " help="Range: [0 - 1]"/>
112
113 <param argument="-w" type="integer" optional="true" min="0" label="Window frame size - general" help="score of position i is the average of the window (i - n) to (i + n). Will override specific sizes set below"/> 111 <param argument="-w" type="integer" optional="true" min="0" label="Window frame size - general" help="score of position i is the average of the window (i - n) to (i + n). Will override specific sizes set below"/>
114 <param argument="-gw" type="integer" optional="true" min="0" label="Window frame size applied to Gaps" help="score of position i is the average of the window (i - n) to (i + n)."/> 112 <param argument="-gw" type="integer" optional="true" min="0" label="Window frame size applied to Gaps" help="score of position i is the average of the window (i - n) to (i + n)."/>
115 <param argument="-sw" type="integer" optional="true" min="0" label="Window frame size applied to Similarity" help="score of position i is the average of the window (i - n) to (i + n)."/> 113 <param argument="-sw" type="integer" optional="true" min="0" label="Window frame size applied to Similarity" help="score of position i is the average of the window (i - n) to (i + n)."/>
116 <param argument="-cw" type="integer" optional="true" min="0" label="Window frame size applied to Consistency" help="score of position i is the average of the window (i - n) to (i + n)."/> 114 <param argument="-cw" type="integer" optional="true" min="0" label="Window frame size applied to Consistency" help="score of position i is the average of the window (i - n) to (i + n)."/>
117
118
119 </when> 115 </when>
120 </conditional> 116 </conditional>
121 <param argument="-resoverlap" type="float" optional="true" min="0" max="1" label="Residue overlap" help="Minimum overlap of a positions with other positions in the column to be considered a “good position”. Range: [0-1]. Must be used in combination with Sequence overlap."/> 117 <param argument="-resoverlap" type="float" optional="true" min="0" max="1" label="Residue overlap" help="Minimum overlap of a positions with other positions in the column to be considered a “good position”. Range: [0-1]. Must be used in combination with Sequence overlap."/>
122 <param argument="-seqoverlap" type="integer" optional="true" min="0" max="100" label="Sequence overlap" help="Minimum percentage of “good positions” that a sequence must have in order to be conserved. Range: [0-100]. Must be used in combination with Residue overlap."/> 118 <param argument="-seqoverlap" type="integer" optional="true" min="0" max="100" label="Sequence overlap" help="Minimum percentage of “good positions” that a sequence must have in order to be conserved. Range: [0-100]. Must be used in combination with Residue overlap."/>
123 119
137 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> 133 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option>
138 </param> 134 </param>
139 <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/> 135 <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/>
140 </inputs> 136 </inputs>
141 <outputs> 137 <outputs>
142 <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment."> 138 <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment">
143 <change_format> 139 <change_format>
144 <when input="out_format_selector" value="-fasta" format="fasta" /> 140 <when input="out_format_selector" value="-fasta" format="fasta"/>
145 <when input="out_format_selector" value="-fasta_m10" format="fasta" /> 141 <when input="out_format_selector" value="-fasta_m10" format="fasta"/>
146 <when input="out_format_selector" value="-phylip" format="phylip" /> 142 <when input="out_format_selector" value="-phylip" format="phylip"/>
147 <when input="out_format_selector" value="-phylip_m10" format="phylip" /> 143 <when input="out_format_selector" value="-phylip_m10" format="phylip"/>
148 <when input="out_format_selector" value="-phylip_paml" format="phylip" /> 144 <when input="out_format_selector" value="-phylip_paml" format="phylip"/>
149 <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" /> 145 <when input="out_format_selector" value="-phylip_paml_m10" format="phylip"/>
150 <when input="out_format_selector" value="-phylip3.2" format="phylip" /> 146 <when input="out_format_selector" value="-phylip3.2" format="phylip"/>
151 <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" /> 147 <when input="out_format_selector" value="-phylip3.2_m10" format="phylip"/>
152 <when input="out_format_selector" value="-clustal" format="clustal" /> 148 <when input="out_format_selector" value="-clustal" format="clustal"/>
153 <when input="out_format_selector" value="-mega" format="mega" /> 149 <when input="out_format_selector" value="-mega" format="mega"/>
154 <when input="out_format_selector" value="-nbrf" format="pir" /> 150 <when input="out_format_selector" value="-nbrf" format="pir"/>
155 <when input="out_format_selector" value="-nexus" format="nexus" /> 151 <when input="out_format_selector" value="-nexus" format="nexus"/>
156 </change_format> 152 </change_format>
157 </data> 153 </data>
158 <data name="html_summary" format="html" label="${tool.name} on ${on_string}: HTML report"> 154 <data name="html_summary" format="html" label="${tool.name} on ${on_string}: HTML report">
159 <filter> trimming_mode['mode_selector'] != 'manual' </filter> 155 <filter> trimming_mode['mode_selector'] != 'manual' </filter>
160 </data> 156 </data>
161 <data name="statsout" format="txt" label="${tool.name} on ${on_string}: statistics"> 157 <data name="statsout" format="txt" label="${tool.name} on ${on_string}: Statistics">
162 <filter> statistics </filter> 158 <filter> statistics </filter>
163 </data> 159 </data>
164 </outputs> 160 </outputs>
165 <tests> 161 <tests>
166 <test expect_num_outputs="2"><!-- test automated trim setting --> 162 <!-- Test 01: automated trim setting -->
163 <test expect_num_outputs="2">
167 <param name="in" value="example.009.AA.fasta"/> 164 <param name="in" value="example.009.AA.fasta"/>
168 <param name="mode_selector" value="-gappyout" /> 165 <conditional name="trimming_mode">
169 <param name="out_format_selector" value="-mega" /> 166 <param name="mode_selector" value="-gappyout"/>
167 </conditional>
168 <param name="out_format_selector" value="-mega"/>
170 <output name="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/> 169 <output name="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/>
171 <output name="html_summary" file="trimmed_example.009.AA.html" ftype="html"/> 170 <output name="html_summary" file="trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
172 </test> 171 </test>
173 <test expect_num_outputs="2"><!-- test custom trim setting --> 172 <!-- Test 02: custom trim setting -->
173 <test expect_num_outputs="2">
174 <param name="in" value="example.009.AA.fasta"/> 174 <param name="in" value="example.009.AA.fasta"/>
175 <param name="mode_selector" value="custom" /> 175 <conditional name="trimming_mode">
176 <param name="gapthreshold" value="0.5" /> 176 <param name="mode_selector" value="custom"/>
177 <param name="simthreshold" value="0.5" /> 177 <param name="gapthreshold" value="0.5"/>
178 <param name="cons" value="5" /> 178 <param name="simthreshold" value="0.5"/>
179 <param name="out_format_selector" value="-phylip_paml_m10" /> 179 <param name="cons" value="5"/>
180 </conditional>
181 <param name="out_format_selector" value="-phylip_paml_m10"/>
180 <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/> 182 <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>
181 <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/> 183 <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
182 </test> 184 </test>
183 <test expect_num_outputs="2"><!-- test additionalcustom trim setting --> 185 <!-- Test 03: additional custom trim setting -->
186 <test expect_num_outputs="2">
184 <param name="in" value="example.009.AA.fasta"/> 187 <param name="in" value="example.009.AA.fasta"/>
185 <param name="mode_selector" value="custom" /> 188 <conditional name="trimming_mode">
186 <param name="gapthreshold" value="0.75" /> 189 <param name="mode_selector" value="custom"/>
187 <param name="simthreshold" value="0.8" /> 190 <param name="gapthreshold" value="0.75"/>
188 <param name="cons" value="5" /> 191 <param name="simthreshold" value="0.8"/>
189 <param name="conthreshold" value="0.5" /> 192 <param name="cons" value="5"/>
190 <param name="clusters" value="4" /> 193 <param name="conthreshold" value="0.5"/>
191 <param name="maxidentity" value="0.8" /> 194 <param name="clusters" value="4"/>
192 <param name="out_format_selector" value="-nexus" /> 195 <param name="maxidentity" value="0.8"/>
196 </conditional>
197 <param name="out_format_selector" value="-nexus"/>
193 <output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/> 198 <output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/>
194 <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html"/> 199 <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
195 </test> 200 </test>
196 <test expect_num_outputs="2"><!-- test window settings --> 201 <!-- Test 04: Window settings -->
202 <test expect_num_outputs="2">
197 <param name="in" value="example.005.AA.fasta"/> 203 <param name="in" value="example.005.AA.fasta"/>
198 <param name="mode_selector" value="custom" /> 204 <conditional name="trimming_mode">
199 <param name="gapthreshold" value="0.5" /> 205 <param name="mode_selector" value="custom"/>
200 <param name="simthreshold" value="0.5" /> 206 <param name="gapthreshold" value="0.5"/>
201 <param name="conthreshold" value="0.5" /> 207 <param name="simthreshold" value="0.5"/>
202 <param name="gw" value="3"/> 208 <param name="conthreshold" value="0.5"/>
203 <param name="sw" value="4"/> 209 <param name="gw" value="3"/>
204 <param name="cw" value="5"/> 210 <param name="sw" value="4"/>
211 <param name="cw" value="5"/>
212 </conditional>
205 <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/> 213 <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/>
206 <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html"/> 214 <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html" lines_diff="4"/>
207 </test> 215 </test>
208 <test expect_num_outputs="3"><!-- test with phylip input and output statistics --> 216 <!-- Test 05: with phylip input and output statistics -->
217 <test expect_num_outputs="3">
209 <param name="in" value="example.002.AA.phy" ftype="phylip"/> 218 <param name="in" value="example.002.AA.phy" ftype="phylip"/>
210 <param name="mode_selector" value="-strict"/> 219 <conditional name="trimming_mode">
220 <param name="mode_selector" value="-strict"/>
221 </conditional>
211 <param name="statistics" value="true"/> 222 <param name="statistics" value="true"/>
212 <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip" lines_diff="0"/> 223 <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip"/>
213 <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="0"/> 224 <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="4"/>
214 <output name="statsout" file="example.002.AA.stats.txt" ftype="txt" lines_diff="0"/> 225 <output name="statsout" file="example.002.AA.stats.txt" ftype="txt"/>
215 </test> 226 </test>
216 <test expect_num_outputs="2"><!-- test with overlap trimming --> 227 <!-- Test 06: with overlap trimming -->
228 <test expect_num_outputs="2">
217 <param name="in" value="example.005.AA.fasta" ftype="fasta"/> 229 <param name="in" value="example.005.AA.fasta" ftype="fasta"/>
218 <param name="mode_selector" value="-nogaps"/> 230 <conditional name="trimming_mode">
231 <param name="mode_selector" value="-nogaps"/>
232 </conditional>
219 <param name="resoverlap" value="0.8"/> 233 <param name="resoverlap" value="0.8"/>
220 <param name="seqoverlap" value="6"/> 234 <param name="seqoverlap" value="6"/>
221 <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta" lines_diff="0"/> 235 <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta"/>
222 <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="0"/> 236 <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="4"/>
223 </test> 237 </test>
224 <test expect_num_outputs="1"><!-- test with manual trimming --> 238 <!-- Test 07: with manual trimming -->
239 <test expect_num_outputs="1">
225 <param name="in" value="example.009.AA.fasta" ftype="fasta"/> 240 <param name="in" value="example.009.AA.fasta" ftype="fasta"/>
226 <param name="mode_selector" value="manual"/> 241 <conditional name="trimming_mode">
227 <param name="selectcols" value="2,4,7-9"/> 242 <param name="mode_selector" value="manual"/>
228 <param name="selectseqs" value="1,3,5-7"/> 243 <param name="selectcols" value="2,4,7-9"/>
229 <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta" lines_diff="0"/> 244 <param name="selectseqs" value="1,3,5-7"/>
245 </conditional>
246 <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta"/>
230 </test> 247 </test>
231 </tests> 248 </tests>
232 <help><![CDATA[ 249 <help><![CDATA[
233 250
234 TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. 251 TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.